Biotechnology information and knowledge grid

European Commission Directorate-General For The Information Society And Media

Description

BioGrid
Information technology and telecommunications
Target audience: Specialised/Technical

Sujets

• Information technology
• Information society (disambiguation)
• Computer software
• Biotechnology
• Informatique
• Marketing et communication

Informations

• Publié par: EUROPEAN-COMMISSION-DIRECTORATE-GENERAL-FOR-THE-INFORMATION-SOCIETY-AND-MEDIA
• Nombre de lectures: 8
• Langue: English

Extrait

Framework Programme 5Grid projects - Achievements

Biotechnology Information and Knowledge Grid

BioGrid

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Scope With bioinformatics data growing exponentially, there is a tremendous need for data and systems integration.The problem is that despite there being a wealth of data available to help biologists working on diseases like osteoporosis, such data is likely to be in geographically distributed sources, in different formats and will probably require further computation to be useful for analysis by the biologist.The BioGrid solution has been to develop a prototype which integrates gene expression data, protein interaction data and text mining in a manner not previously available.

Innovation and functionality The BioGrid prototype integrates gene expression data with protein interaction data and literature data.This prototype allows biologists to map their gene expression data on to a protein interaction network consisting of over 40 000 structural protein interactions. Next, the user can mine the literature for relevant interactions discovered in the interaction network. The BioGrid approach is novel as it links genomics to proteomics and text mining.Thenal text-mining step deploys a novel approach using the gene ontology to explore the literature search results.Thus it provides a fast and structured overview of the relevant literature. BioGrids main achievement is the development and evaluation of the BioGrid prototype, whichexibly integrates gene expression data, protein interaction data, and literature data.The prototype was evaluated together with biologists from the Medical Research Council, Cambridge, United Kingdom, and the Biotec of TU Dresden on two biological use cases (energy-related genes and complex I, relevant for diabetes) and gene expression during osteoclast differentiation (relevant for bone diseases such as osteoporosis). BioGrid has developed the Prova language for rule-based Java-scripting language. Prova has been made open source and has attracted already over 20 developers from three continents including BioWisdom Ltd, a bioinformatics start-up based in Cambridge, UK. To achieve aexible integration of BioGrid modules, a meta-model was developed which captures the architecture of the system at the highest possible level and thus reduces the complexity of introducing new modules. The power of the approach was documented by adding an additional interaction space based on experimental rather than structure data and an additional literature space. Groningen has founded a spin-off and obtained seed funding through the Dutch BioPartner initiative using the meta-model as part of their gene expression data management platform.

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BioGRID

Contract number IST-2000-25406 Type of project Cost-shared Research and Technological Development Action

Project coordinator The Biotechnological Centre (BioZ), Technical University Dresden Contact person Prof. Dr. Michael Shroeder Biotechnologisches Zentrum TU Dresden D-01062 Dresden [e-mail]

Maximum Community contribution to project EUR 834 000

Project start date 1 September 2002

Duration 27 months

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